BN0602 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.6162e-06 1.0365e-04
Layer 5 4.0935e-06 3.4946e-04
Layer 1 7.0894e-06 3.5583e-02
Layer 2 1.2371e-04 6.7182e-03
WM 6.7869e-04 6.1602e-02
Layer 6 1.1271e-03 1.9356e-03

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 3.5586 0.6707
SLC17A7 Layer 6 3.3066 0.6688
CALM3 Layer 3 3.1172 0.6611
MTCH1 Layer 5 2.7070 0.6492
PRKAR1B Layer 6 3.1934 0.6429
CAPNS1 Layer 3 2.7158 0.6407
DNM1 Layer 3 3.5352 0.6402
RTN3 Layer 6 3.3008 0.6385
PEBP1 Layer 3 2.9805 0.6376
BASP1 Layer 5 3.2500 0.6375
SNCB Layer 6 3.6367 0.6364
SCAMP5 Layer 5 2.4512 0.6363
YWHAH Layer 6 3.2012 0.6317
CHN1 Layer 3 3.6523 0.6297
SNAP25 Layer 6 3.9805 0.6296
APBB1 Layer 6 3.0000 0.6296
TUBA1B Layer 5 2.7305 0.6258
EEF1A2 Layer 6 3.6133 0.6238
PKM Layer 3 2.7188 0.6218
CALM2 Layer 3 2.8906 0.6203
GDI1 Layer 6 2.9473 0.6202
TSPAN3 Layer 3 2.8428 0.6200
ATP6V0C Layer 6 2.6660 0.6181
AP2M1 Layer 6 2.8516 0.6176
KLC1 Layer 6 2.7129 0.6152
OLFM1 Layer 3 3.0645 0.6150
DMTN Layer 5 2.6836 0.6139
EPHB6 Layer 5 2.4570 0.6133
SYN1 Layer 3 3.7676 0.6113
PPP2R1A Layer 3 2.8906 0.6112
CLSTN1 Layer 3 3.2051 0.6110
PSAP Layer 6 2.8516 0.6108
RTN1 Layer 6 4.4688 0.6105
YWHAB Layer 5 2.8516 0.6101
CFL1 Layer 6 2.9863 0.6099
RAB6B Layer 6 3.8965 0.6094
GUK1 Layer 3 2.7070 0.6092
CELF4 Layer 5 2.9473 0.6090
MAST3 Layer 3 2.4893 0.6079
UQCRC1 Layer 6 2.7305 0.6074
ARL6IP1 Layer 6 3.6836 0.6070
EEF2 Layer 3 2.8281 0.6070
PLD3 Layer 3 3.1523 0.6068
NCAM1 Layer 6 3.0918 0.6066
TSC22D1 Layer 3 2.9697 0.6055
ATP9A Layer 6 2.7188 0.6054
PREPL Layer 3 2.7715 0.6052
NRXN2 Layer 3 2.5664 0.6038
COX5B Layer 6 3.4531 0.6033
TPI1 Layer 5 2.6602 0.6029

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0602
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0602_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0602/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0602/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0602/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0602/report/PD/BN0602_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0602/report/PD/BN0602_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:32:51
  • Number of Processes: 10
  • Spending Time: 0h 3m